Abstract: In local comprehensive colleges and universities, due to the limitation caused by special characteristics of medical discipline, its development has been restricted to some extent. With the proposal of the national "2011 plan", collaborative innovation has become a new mode for developing colleges and universities, and the construction of medical disciplines must be closely integrated with collaborative innovation. Therefore, a new collaborative innovation system is to be constructed by the following measures: to streamline the new collaborative innovation system by means of strengthening organizational leadership and coordination; to construct echelon of discipline by focusing on the selection of academic leaders and multi-measures; to adapt to the internal demand of discipline development by encouraging interdisciplinary integration and creating a platform for training compound talents to promote the level of discipline; to enhance the construction of collaborative innovation center to promote the development of disciplines and actively serve the industry to create characteristic courses; to integrate into local areas and strengthen cooperation with enterprises and research institutions so as to expand the scope of exchanges and intensify the cooperation. By intensifying internal and external collaboration of the university, the level of medical discipline construction in local comprehensive colleges and universities will be enhanced.